Elements required for an efficient NADP-malic enzyme type C4 photosynthesis

From leaf to multiscale models of photosynthesis: applications and challenges for crop improvement

To keep up with the growth of human population and to circumvent deleterious effects of global climate change, it is essential to enhance crop yield to achieve higher production. Here we review mathematical models of oxygenic photosynthesis that are extensively used, and discuss in depth a subset that accounts for diverse approaches providing solutions to our objective. These include models (1) to study different ways to enhance photosynthesis, such as fine-tuning antenna size, photoprotection and electron transport; (2) to bioengineer carbon metabolism; and (3) to evaluate the interactions between the process of photosynthesis and the seasonal crop dynamics, or those that have included statistical whole-genome prediction methods to quantify the impact of photosynthesis traits on the improvement of crop yield. We conclude by emphasizing that the results obtained in these studies clearly demonstrate that mathematical modelling is a key tool to examine different approaches to improve photosynthesis for better productivity, while effective multiscale crop models, especially those that also include remote sensing data, are indispensable to verify different strategies to obtain maximized crop yields.

Overexpression of chloroplastic Zea mays NADP-malic enzyme (ZmNADP-ME) confers tolerance to salt stress in Arabidopsis thaliana

The C4 plants photosynthesize better than C3 plants especially in arid environment. As an attempt to genetically convert C3 plant to C4, the cDNA of decarboxylating C4 type NADP-malic enzyme from Zea mays (ZmNADP-ME) that has lower Km for malate and NADP than its C3 isoforms, was overexpressed in Arabidopsis thaliana under the control of 35S promoter. Due to increased activity of NADP-ME in the transgenics the malate decarboxylation increased that resulted in loss of carbon skeletons needed for amino acid and protein synthesis. Consequently, amino acid and protein content of the transgenics declined. Therefore, the Chl content, photosynthetic efficiency (Fv/Fm), electron transport rate (ETR), the quantum yield of photosynthetic CO2 assimilation, rosette diameter, and biomass were lower in the transgenics. However, in salt stress (150 mM NaCl), the overexpressers had higher Chl, protein content, Fv/Fm, ETR, and biomass than the vector control. NADPH generated in the transgenics due to increased malate decarboxylation, contributed to augmented synthesis of proline, the osmoprotectant required to alleviate the reactive oxygen species-mediated membrane damage and oxidative stress. Consequently, the glutathione peroxidase activity increased and H2O2 content decreased in the salt-stressed transgenics. The reduced membrane lipid peroxidation and lower malondialdehyde production resulted in better preservation, of thylakoid integrity and membrane architecture in the transgenics under saline environment. Our results clearly demonstrate that overexpression of C4 chloroplastic ZmNADP-ME in the C3 Arabidopsis thaliana, although decrease their photosynthetic efficiency, protects the transgenics from salinity stress.

Lessons from relatives: C4 photosynthesis enhances CO2 assimilation during the low-light phase of fluctuations

Despite the global importance of species with C4 photosynthesis, there is a lack of consensus regarding C4 performance under fluctuating light. Contrasting hypotheses and experimental evidence suggest that C4 photosynthesis is either less or more efficient in fixing carbon under fluctuating light than the ancestral C3 form. Two main issues have been identified that may underly the lack of consensus: neglect of evolutionary distance between selected C3 and C4 species and use of contrasting fluctuating light treatments. To circumvent these issues, we measured photosynthetic responses to fluctuating light across 3 independent phylogenetically controlled comparisons between C3 and C4 species from Alloteropsis, Flaveria, and Cleome genera under 21% and 2% O2. Leaves were subjected to repetitive stepwise changes in light intensity (800 and 100 µmol m-2 s-1 photon flux density) with 3 contrasting durations: 6, 30, and 300 s. These experiments reconciled the opposing results found across previous studies and showed that (i) stimulation of CO2 assimilation in C4 species during the low-light phase was both stronger and more sustained than in C3 species; (ii) CO2 assimilation patterns during the high-light phase could be attributable to species or C4 subtype differences rather than photosynthetic pathway; and (iii) the duration of each light step in the fluctuation regime can strongly influence experimental outcomes.

Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana

Terrestrial CAM plants typically occur in hot semiarid regions, yet can show high crop productivity under favorable conditions. To achieve a more mechanistic understanding of CAM plant productivity, a biochemical model of diel metabolism was developed and integrated with 3-D shoot morphology to predict the energetics of light interception and photosynthetic carbon assimilation. Using Agave tequilana as an example, this biochemical model faithfully simulated the four diel phases of CO2 and metabolite dynamics during the CAM rhythm. After capturing the 3-D form over an 8-yr production cycle, a ray-tracing method allowed the prediction of the light microclimate across all photosynthetic surfaces. Integration with the biochemical model thereby enabled the simulation of plant and stand carbon uptake over daily and annual courses. The theoretical maximum energy conversion efficiency of Agave spp. is calculated at 0.045-0.049, up to 7% higher than for C3 photosynthesis. Actual light interception, and biochemical and anatomical limitations, reduced this to 0.0069, or 15.6 Mg ha-1  yr-1 dry mass annualized over an 8-yr cropping cycle, consistent with observation. This is comparable to the productivity of many C3 crops, demonstrating the potential of CAM plants in climates where little else may be grown while indicating strategies that could raise their productivity.

Activation of CO2 assimilation during photosynthetic induction is slower in C4 than in C3 photosynthesis in three phylogenetically controlled experiments

INTRODUCTION

Despite their importance for the global carbon cycle and crop production, species with C₄ photosynthesis are still somewhat understudied relative to C₃ species. Although the benefits of the C₄ carbon concentrating mechanism are readily observable under optimal steady state conditions, it is less clear how the presence of C₄ affects activation of CO₂ assimilation during photosynthetic induction.

METHODS

In this study we aimed to characterise differences between C₄ and C₃ photosynthetic induction responses by analysing steady state photosynthesis and photosynthetic induction in three phylogenetically linked pairs of C₃ and C₄ species from Alloteropsis, Flaveria, and Cleome genera. Experiments were conducted both at 21% and 2% O₂ to evaluate the role of photorespiration during photosynthetic induction.

RESULTS

Our results confirm C₄ species have slower activation of CO₂ assimilation during photosynthetic induction than C₃ species, but the apparent mechanism behind these differences varied between genera. Incomplete suppression of photorespiration was found to impact photosynthetic induction significantly in C₄ Flaveria bidentis, whereas in the Cleome and Alloteropsis C₄ species, delayed activation of the C₃ cycle appeared to limit induction and a potentially supporting role for photorespiration was also identified.

DISCUSSION

The sheer variation in photosynthetic induction responses observed in our limited sample of species highlights the importance of controlling for evolutionary distance when comparing C₃ and C₄ photosynthetic pathways.

Two major metabolic factors for an efficient NADP-malic enzyme type C4 photosynthesis

Compared to the large number of studies focused on the factors controlling C3 photosynthesis efficiency, there are relatively fewer studies of the factors controlling photosynthetic efficiency in C4 leaves. Here, we used a dynamic systems model of C4 photosynthesis based on maize (Zea mays) to identify features associated with high photosynthetic efficiency in NADP-malic enzyme (NADP-ME) type C4 photosynthesis. We found that two additional factors related to coordination between C4 shuttle metabolism and C3 metabolism are required for efficient C4 photosynthesis: (1) accumulating a high concentration of phosphoenolpyruvate through maintaining a large PGA concentration in the mesophyll cell chloroplast and (2) maintaining a suitable oxidized status in bundle sheath cell chloroplasts. These identified mechanisms are in line with the current cellular location of enzymes/proteins involved in the starch synthesis, the Calvin-Benson cycle and photosystem II of NADP-ME type C4 photosynthesis. These findings suggested potential strategies for improving C4 photosynthesis and engineering C4 rice.

Elucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

Biocatalytic fumarate synthesis from pyruvate and CO2 as a feedstock

The biocatalytic synthesis of fumarate from CO2 and pyruvate vial-malate as an intermediate in an aqueous medium using a biocatalytic system consisting of malate dehydrogenase and fumarase in the presence of NADH is developed.

A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments

While flux balance analysis (FBA) provides a framework for predicting steady-state leaf metabolic network fluxes, it does not readily capture the response to environmental variables without being coupled to other modelling formulations. To address this, we coupled an FBA model of 903 reactions of soybean (Glycine max) leaf metabolism with e-photosynthesis, a dynamic model that captures the kinetics of 126 reactions of photosynthesis and associated chloroplast carbon metabolism. Successful coupling was achieved in an iterative formulation in which fluxes from e-photosynthesis were used to constrain the FBA model and then, in turn, fluxes computed from the FBA model used to update parameters in e-photosynthesis. This process was repeated until common fluxes in the two models converged. Coupling did not hamper the ability of the kinetic module to accurately predict the carbon assimilation rate, photosystem II electron flux, and starch accumulation of field-grown soybean at two CO2 concentrations. The coupled model also allowed accurate predictions of additional parameters such as nocturnal respiration, as well as analysis of the effect of light intensity and elevated CO2 on leaf metabolism. Predictions included an unexpected decrease in the rate of export of sucrose from the leaf at high light, due to altered starch-sucrose partitioning, and altered daytime flux modes in the tricarboxylic acid cycle at elevated CO2 . Mitochondrial fluxes were notably different between growing and mature leaves, with greater anaplerotic, tricarboxylic acid cycle and mitochondrial ATP synthase fluxes predicted in the former, primarily to provide carbon skeletons and energy for protein synthesis.

The limiting factors and regulatory processes that control the environmental responses of C3, C3-C4 intermediate, and C4 photosynthesis

Here, we describe a model of C3, C3-C4 intermediate, and C4 photosynthesis that is designed to facilitate quantitative analysis of physiological measurements. The model relates the factors limiting electron transport and carbon metabolism, the regulatory processes that coordinate these metabolic domains, and the responses to light, carbon dioxide, and temperature. It has three unique features. First, mechanistic expressions describe how the cytochrome b6f complex controls electron transport in mesophyll and bundle sheath chloroplasts. Second, the coupling between the mesophyll and bundle sheath expressions represents how feedback regulation of Cyt b6f coordinates electron transport and carbon metabolism. Third, the temperature sensitivity of Cyt b6f is differentiated from that of the coupling between NADPH, Fd, and ATP production. Using this model, we present simulations demonstrating that the light dependence of the carbon dioxide compensation point in C3-C4 leaves can be explained by co-occurrence of light saturation in the mesophyll and light limitation in the bundle sheath. We also present inversions demonstrating that population-level variation in the carbon dioxide compensation point in a Type I C3-C4 plant, Flaveria chloraefolia, can be explained by variable allocation of photosynthetic capacity to the bundle sheath. These results suggest that Type I C3-C4 intermediate plants adjust pigment and protein distributions to optimize the glycine shuttle under different light and temperature regimes, and that the malate and aspartate shuttles may have originally functioned to smooth out the energy supply and demand associated with the glycine shuttle. This model has a wide range of potential applications to physiological, ecological, and evolutionary questions.

Potential metabolic mechanisms for inhibited chloroplast nitrogen assimilation under high CO2

Improving photosynthesis is considered a major and feasible option to dramatically increase crop yield potential. Increased atmospheric CO2 concentration often stimulates both photosynthesis and crop yield, but decreases protein content in the main C3 cereal crops. This decreased protein content in crops constrains the benefits of elevated CO2 on crop yield and affects their nutritional value for humans. To support studies of photosynthetic nitrogen assimilation and its complex interaction with photosynthetic carbon metabolism for crop improvement, we developed a dynamic systems model of plant primary metabolism, which includes the Calvin-Benson cycle, the photorespiration pathway, starch synthesis, glycolysis-gluconeogenesis, the tricarboxylic acid cycle, and chloroplastic nitrogen assimilation. This model successfully captures responses of net photosynthetic CO2 uptake rate (A), respiration rate, and nitrogen assimilation rate to different irradiance and CO2 levels. We then used this model to predict inhibition of nitrogen assimilation under elevated CO2. The potential mechanisms underlying inhibited nitrogen assimilation under elevated CO2 were further explored with this model. Simulations suggest that enhancing the supply of α-ketoglutarate is a potential strategy to maintain high rates of nitrogen assimilation under elevated CO2. This model can be used as a heuristic tool to support research on interactions between photosynthesis, respiration, and nitrogen assimilation. It also provides a basic framework to support the design and engineering of C3 plant primary metabolism for enhanced photosynthetic efficiency and nitrogen assimilation in the coming high-CO2 world.

Role of bundle sheath conductance in sustaining photosynthesis competence in sugarcane plants under nitrogen deficiency

The role of bundle sheath conductance (g_bs) in sustaining sugarcane photosynthesis under nitrogen deficiency was investigated. Sugarcane was grown under different levels of nitrogen supply and g_bs was estimated using simultaneous measurements of leaf gas exchange and chlorophyll fluorescence at 21% or 2% [O₂] and varying air [CO₂] and light intensity. Maximum rates of PEPC carboxylation, Rubisco carboxylation, and ATP production increased with an increase in leaf nitrogen concentration (LNC) from 1 to 3 g m^-2. Low nitrogen supply reduced Rubisco and PEPC abundancies, the quantum efficiency of CO₂ assimilation and g_bs. Because of reduced g_bs, low photosynthetic rates were not associated with increased leakiness under nitrogen deficiency. In fact, low nitrogen supply increased bundle sheath cell wall thickness, probably accounting for low g_bs and increased estimates of [CO₂] at Rubisco sites. Effects of nitrogen on expression of ShPIP2;1 and ShPIP1;2 aquaporins did not explain changes in g_bs. Our data revealed that reduced Rubisco carboxylation was the main factor causing low sugarcane photosynthesis at low nitrogen supply, in contrast to the previous report on the importance of an impaired CO₂ concentration mechanism under N deficiency. Our findings suggest higher investment of nitrogen into Rubisco protein would favour photosynthesis and plant performance under low nitrogen availability.

Global Identification and Systematic Analysis of Lysine Malonylation in Maize (Zea mays L.)

Lysine malonylation is a kind of post-translational modifications (PTMs) discovered in recent years, which plays an important regulatory role in plants. Maize (Zea mays L.) is a major global cereal crop. Immunoblotting revealed that maize was rich in malonylated proteins. We therefore performed a qualitative malonylome analysis to globally identify malonylated proteins in maize. In total, 1,722 uniquely malonylated lysine residues were obtained in 810 proteins. The modified proteins were involved in various biological processes such as photosynthesis, ribosome and oxidative phosphorylation. Notably, a large proportion of the modified proteins (45%) were located in chloroplast. Further functional analysis revealed that 30 proteins in photosynthesis and 15 key enzymes in the Calvin cycle were malonylated, suggesting an indispensable regulatory role of malonylation in photosynthesis and carbon fixation. This work represents the first comprehensive survey of malonylome in maize and provides an important resource for exploring the function of lysine malonylation in physiological regulation of maize.

Modeling photosynthetic resource allocation connects physiology with evolutionary environments

The regulation of resource allocation in biological systems observed today is the cumulative result of natural selection in ancestral and recent environments. To what extent are observed resource allocation patterns in different photosynthetic types optimally adapted to current conditions, and to what extent do they reflect ancestral environments? Here, we explore these questions for C₃, C₄, and C₃–C₄ intermediate plants of the model genus Flaveria. We developed a detailed mathematical model of carbon fixation, which accounts for various environmental parameters and for energy and nitrogen partitioning across photosynthetic components. This allows us to assess environment-dependent plant physiology and performance as a function of resource allocation patterns. Models of C₄ plants optimized for conditions experienced by evolutionary ancestors perform better than models accounting for experimental growth conditions, indicating low phenotypic plasticity. Supporting this interpretation, the model predicts that C₄ species need to re-allocate more nitrogen between photosynthetic components than C₃ species to adapt to new environments. We thus hypothesize that observed resource distribution patterns in C₄ plants still reflect optimality in ancestral environments, allowing the quantitative inference of these environments from today’s plants. Our work allows us to quantify environmental effects on photosynthetic resource allocation and performance in the light of evolutionary history.

The coordination of major events in C4 photosynthesis evolution in the genus Flaveria

C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex traits and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis. We first mapped transcript abundance, protein sequence and morphological features onto the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features; we then predicted the relative changes of ancestral nodes of those features to illustrate the major events during the evolution of C4 photosynthesis. We found that gene expression and protein sequence showed consistent modification patterns in the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed. The greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species. Our results show highly coordinated changes in gene expression, protein sequence and morphological features, which support evolutionary major events during the evolution of C4 metabolism.

Towards a dynamic photosynthesis model to guide yield improvement in C4 crops

The most productive C4 food and biofuel crops, such as Saccharum officinarum (sugarcane), Sorghum bicolor (sorghum) and Zea mays (maize), all use NADP-ME-type C4 photosynthesis. Despite high productivities, these crops fall well short of the theoretical maximum solar conversion efficiency of 6%. Understanding the basis of these inefficiencies is key for bioengineering and breeding strategies to increase the sustainable productivity of these major C4 crops. Photosynthesis is studied predominantly at steady state in saturating light. In field stands of these crops light is continually changing, and often with rapid fluctuations. Although light may change in a second, the adjustment of photosynthesis may take many minutes, leading to inefficiencies. We measured the rates of CO2 uptake and stomatal conductance of maize, sorghum and sugarcane under fluctuating light regimes. The gas exchange results were combined with a new dynamic photosynthesis model to infer the limiting factors under non-steady-state conditions. The dynamic photosynthesis model was developed from an existing C4 metabolic model for maize and extended to include: (i) post-translational regulation of key photosynthetic enzymes and their temperature responses; (ii) dynamic stomatal conductance; and (iii) leaf energy balance. Testing the model outputs against measured rates of leaf CO2 uptake and stomatal conductance in the three C4 crops indicated that Rubisco activase, the pyruvate phosphate dikinase regulatory protein and stomatal conductance are the major limitations to the efficiency of NADP-ME-type C4 photosynthesis during dark-to-high light transitions. We propose that the level of influence of these limiting factors make them targets for bioengineering the improved photosynthetic efficiency of these key crops.

Efficient Regulation of CO2 Assimilation Enables Greater Resilience to High Temperature and Drought in Maize

Increasing temperatures and extended drought episodes are among the major constraints affecting food production. Maize has a relatively high temperature optimum for photosynthesis compared to C₃ crops, however, the response of this important C₄ crop to the combination of heat and drought stress is poorly understood. Here, we hypothesized that resilience to high temperature combined with water deficit (WD) would require efficient regulation of the photosynthetic traits of maize, including the C₄-CO₂ concentrating mechanism (CCM). Two genotypes of maize with contrasting levels of drought and heat tolerance, B73 and P0023, were acclimatized at high temperature (38°C versus 25°C) under well-watered (WW) or WD conditions. The photosynthetic performance was evaluated by gas exchange and chlorophyll a fluorescence, and in vitro activities of key enzymes for carboxylation (phosphoenolpyruvate carboxylase), decarboxylation (NADP-malic enzyme), and carbon fixation (Rubisco). Both genotypes successfully acclimatized to the high temperature, although with different mechanisms: while B73 maintained the photosynthetic rates by increasing stomatal conductance (gs), P0023 maintained gs and showed limited transpiration. When WD was experienced in combination with high temperatures, limited transpiration allowed water-savings and acted as a drought stress avoidance mechanism. The photosynthetic efficiency in P0023 was sustained by higher phosphorylated PEPC and electron transport rate (ETR) near vascular tissues, supplying chemical energy for an effective CCM. These results suggest that the key traits for drought and heat tolerance in maize are limited transpiration rate, allied with a synchronized regulation of the carbon assimilation metabolism. These findings can be exploited in future breeding efforts aimed at improving maize resilience to climate change.

A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants

Plants employ photosynthesis to produce sugars for supporting their growth. During photosynthesis, an enzyme Ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) combines its substrate Ribulose 1,5 bisphosphate (RuBP) with CO2 to produce phosphoglycerate (PGA). Alongside, Rubisco also takes up O2 and produce 2-phosphoglycolate (2-PG), a toxic compound broken down into PGA through photorespiration. Photorespiration is not only a resource-demanding process but also results in CO2 loss which affects photosynthetic efficiency in C3 plants. Here, we propose to circumvent photorespiration by adopting the cyanobacterial glycolate decarboxylation pathway into C3 plants. For that, we have integrated the cyanobacterial glycolate decarboxylation pathway into a kinetic model of C3 photosynthetic pathway to evaluate its impact on photosynthesis and photorespiration. Our results show that the cyanobacterial glycolate decarboxylation bypass model exhibits a 10% increase in net photosynthetic rate (A) in comparison with C3 model. Moreover, an increased supply of intercellular CO2 (Ci) from the bypass resulted in a 54.8% increase in PGA while reducing photorespiratory intermediates including glycolate (- 49%) and serine (- 32%). The bypass model, at default conditions, also elucidated a decline in phosphate-based metabolites including RuBP (- 61.3%). The C3 model at elevated level of inorganic phosphate (Pi), exhibited a significant change in RuBP (+ 355%) and PGA (- 98%) which is attributable to the low availability of Ci. Whereas, at elevated Pi, the bypass model exhibited an increase of 73.1% and 33.9% in PGA and RuBP, respectively. Therefore, we deduce a synergistic effect of elevation in CO2 and Pi pool on photosynthesis. We also evaluated the integrative action of CO2, Pi, and Rubisco carboxylation activity (Vcmax) on A and observed that their simultaneous increase raised A by 26%, in the bypass model. Taken together, the study potentiates engineering of cyanobacterial decarboxylation pathway in C3 plants to bypass photorespiration thereby increasing the overall efficiency of photosynthesis.

The Effects of Moderate and Severe Salinity on Composition and Physiology in the Biomass Crop Miscanthus × giganteus

Saline land represents a growing resource that could be utilised for growing biomass crops, such as Miscanthus × giganteus (Greef et Deu.), for eliminating competition with staple food crops. However, the response mechanisms to different salinity regimes, in relation to the impact on quality of the harvested biomass and the combustion properties are largely unknown. Herein, the focus was on the salt-induced compositional changes of ion flux and compartmentalization in the rhizome, stems, and leaves in relation to their impact on salinity tolerance and the combustion quality through investigating the photophysiological, morphophysiological, and biochemical responses of M. × giganteus to moderate and a severe salinity. Severe salinity induced an immediate and sustained adverse response with a reduction in biomass yield, photoinhibition, and metabolic limitations in photosynthesis. Moderate salinity resulted in a slower cumulative response with low biomass losses. Biomass composition, variations in ion compartmentalisation and induction of proline were dependent on the severity and duration of salinity. Ash behaviour indices, including the base percentage and base-to-acid ratio, indicated lower corrosion potential and lower risk of slagging under salinity. Understanding the impact of salinity on the potential for growth on saline land may identify new targets for breeding salinity-tolerant bioenergy crops.

What Matters for C4 Transporters: Evolutionary Changes of Phosphoenolpyruvate Transporter for C4 Photosynthesis

C4 photosynthesis is a complex trait that evolved from its ancestral C3 photosynthesis by recruiting pre-existing genes. These co-opted genes were changed in many aspects compared to their counterparts in C3 species. Most of the evolutionary changes of the C4 shuttle enzymes are well characterized, however, evolutionary changes for the recruited metabolite transporters are less studied. Here we analyzed the evolutionary changes of the shuttle enzyme phosphoenolpyruvate (PEP) transporter (PPT) during its recruitment from C3 to C4 photosynthesis. Our analysis showed that among the two PPT paralogs PPT1 and PPT2, PPT1 was the copy recruited for C4 photosynthesis in multiple C4 lineages. During C4 evolution, PPT1 gained increased transcript abundance, shifted its expression from predominantly in root to in leaf and from bundle sheath cell to mesophyll cell, and gained more rapid and long-lasting responsiveness to light. Modifications occurred in both regulatory and coding regions in C4 PPT1 as compared to C3 PPT1, however, the PEP transporting function of PPT1 remained. We found that PPT1 of a Flaveria C4 species recruited a MEM1 B submodule in the promoter region, which might be related to the increased transcript abundance of PPT1 in C4 mesophyll cells. The case study of PPT further suggested that high transcript abundance in a proper location is of high priority for PPT to support C4 function.

Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models

Mathematical modeling of plant metabolism enables the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In the many studies using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For ¹³C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.

A generalised dynamic model of leaf-level C3 photosynthesis combining light and dark reactions with stomatal behaviour

Global food demand is rising, impelling us to develop strategies for improving the efficiency of photosynthesis. Classical photosynthesis models based on steady-state assumptions are inherently unsuitable for assessing biochemical and stomatal responses to rapid variations in environmental drivers. To identify strategies to increase photosynthetic efficiency, we need models that account for the timing of CO₂ assimilation responses to dynamic environmental stimuli. Herein, I present a dynamic process-based photosynthetic model for C₃ leaves. The model incorporates both light and dark reactions, coupled with a hydro-mechanical model of stomatal behaviour. The model achieved a stable and realistic rate of light-saturated CO₂ assimilation and stomatal conductance. Additionally, it replicated complete typical assimilatory response curves (stepwise change in CO₂ and light intensity at different oxygen levels) featuring both short lag times and full photosynthetic acclimation. The model also successfully replicated transient responses to changes in light intensity (light flecks), CO₂ concentration, and atmospheric oxygen concentration. This dynamic model is suitable for detailed ecophysiological studies and has potential for superseding the long-dominant steady-state approach to photosynthesis modelling. The model runs as a stand-alone workbook in Microsoft® Excel® and is freely available to download along with a video tutorial.

Current and possible approaches for improving photosynthetic efficiency

One of the most important tasks laying ahead today's biotechnology is to improve crop productivity with the aim of meeting increased food and energy demands of humankind. Plant productivity depends on many genetic factors, including life cycle, harvest index, stress tolerance and photosynthetic activity. Many approaches were already tested or suggested to improve either. Limitations of photosynthesis have also been uncovered and efforts been taken to increase its efficiency. Examples include decreasing photosynthetic antennae size, increasing the photosynthetically available light spectrum, countering oxygenase activity of Rubisco by implementing C4 photosynthesis to C3 plants and altering source to sink transport of metabolites. A natural and effective photosynthetic adaptation, the sugar alcohol metabolism got however remarkably little attention in the last years, despite being comparably efficient as C4, and can be considered easier to introduce to new species. We also propose root to shoot carbon-dioxide transport as a means to improve photosynthetic performance and drought tolerance at the same time. Different suggestions and successful examples are covered here for improving plant photosynthesis as well as novel perspectives are presented for future research.

Diffusion of CO2 across the Mesophyll-Bundle Sheath Cell Interface in a C4 Plant with Genetically Reduced PEP Carboxylase Activity

Phosphoenolpyruvate carboxylase (PEPC), localized to the cytosol of the mesophyll cell, catalyzes the first carboxylation step of the C₄ photosynthetic pathway. Here, we used RNA interference to target the cytosolic photosynthetic PEPC isoform in Setaria viridis and isolated independent transformants with very low PEPC activities. These plants required high ambient CO₂ concentrations for growth, consistent with the essential role of PEPC in C₄ photosynthesis. The combination of estimating direct CO₂ fixation by the bundle sheath using gas-exchange measurements and modeling C₄ photosynthesis with low PEPC activity allowed the calculation of bundle sheath conductance to CO₂ diffusion (g_bs ) in the progeny of these plants. Measurements made at a range of temperatures suggested no or negligible effect of temperature on g_bs depending on the technique used to calculate g_bs Anatomical measurements revealed that plants with reduced PEPC activity had reduced cell wall thickness and increased plasmodesmata (PD) density at the mesophyll-bundle sheath (M-BS) cell interface, whereas we observed little difference in these parameters at the mesophyll-mesophyll cell interface. The increased PD density at the M-BS interface was largely driven by an increase in the number of PD pit fields (cluster of PDs) rather than an increase in PD per pit field or the size of pit fields. The correlation of g_bs with bundle sheath surface area per leaf area and PD area per M-BS area showed that these parameters and cell wall thickness are important determinants of g_bs It is intriguing to speculate that PD development is responsive to changes in C₄ photosynthetic flux.

Strategies and tools to improve crop productivity by targeting photosynthesis

Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.

Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity

The triose-phosphate/phosphate translocator (TPT) catalyses the strict 1:1 exchange of triose-phosphate, 3-phosphoglycerate and inorganic phosphate across the chloroplast envelope, and plays crucial roles in photosynthesis. Despite rigorous study for more than 40 years, the molecular mechanism of TPT is poorly understood because of the lack of structural information. Here we report crystal structures of TPT bound to two different substrates, 3-phosphoglycerate and inorganic phosphate, in occluded conformations. The structures reveal that TPT adopts a 10-transmembrane drug/metabolite transporter fold. Both substrates are bound within the same central pocket, where conserved lysine, arginine and tyrosine residues recognize the shared phosphate group. A structural comparison with the outward-open conformation of the bacterial drug/metabolite transporter suggests a rocker-switch motion of helix bundles, and molecular dynamics simulations support a model in which this rocker-switch motion is tightly coupled to the substrate binding, to ensure strict 1:1 exchange. These results reveal the unique mechanism of sugar phosphate/phosphate exchange by TPT.

Kinetic Modeling of Photorespiration

Dynamic systems modeling is a method to study systematic properties of a complex system. The basic principles, procedures, and tools available to develop a dynamic systems model of complex metabolic processes are detailed. Here, a photosynthetic carbon metabolism model, which includes the Calvin Benson cycle, photorespiration, and starch and sucrose synthesis pathways, is used as an example to illustrate the whole process of model development.

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

C4 photosynthesis in C3 rice: a theoretical analysis of biochemical and anatomical factors

Engineering C₄ photosynthesis into rice has been considered a promising strategy to increase photosynthesis and yield. A question that remains to be answered is whether expressing a C₄ metabolic cycle into a C₃ leaf structure and without removing the C₃ background metabolism improves photosynthetic efficiency. To explore this question, we developed a 3D reaction diffusion model of bundle-sheath and connected mesophyll cells in a C₃ rice leaf. Our results show that integrating a C₄ metabolic pathway into rice leaves with a C₃ metabolism and mesophyll structure may lead to an improved photosynthesis under current ambient CO₂ concentration. We analysed a number of physiological factors that influence the CO₂ uptake rate, which include the chloroplast surface area exposed to intercellular air space, bundle-sheath cell wall thickness, bundle-sheath chloroplast envelope permeability, Rubisco concentration and the energy partitioning between C₃ and C₄ cycles. Among these, partitioning of energy between C₃ and C₄ photosynthesis and the partitioning of Rubisco between mesophyll and bundle-sheath cells are decisive factors controlling photosynthetic efficiency in an engineered C₃ -C₄ leaf. The implications of the results for the sequence of C₄ evolution are also discussed.

Cross species selection scans identify components of C4 photosynthesis in the grasses

C4 photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C4 lineages to facilitate discovery of C4 genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C3 panicoid grass, Dichanthelium oligosanthes This method, in contrast to previous studies, does not rely on any a priori knowledge of the genes that contribute to biochemical or anatomical innovations associated with C4 photosynthesis. We identified a list of 88 candidate genes that include both known and potentially novel components of the C4 pathway. This set includes the carbon shuttle enzymes pyruvate, phosphate dikinase, phosphoenolpyruvate carboxylase and NADP malic enzyme as well as several predicted transporter proteins that likely play an essential role in promoting the flux of metabolites between the bundle sheath and mesophyll cells. Importantly, this approach demonstrates the application of fundamental molecular evolution principles to dissect the genetic basis of a complex photosynthetic adaptation in plants. Furthermore, we demonstrate how the output of the selection scans can be combined with expression data to provide additional power to prioritize candidate gene lists and suggest novel opportunities for pathway engineering.

A generalized stoichiometric model of C3, C2, C2+C4, and C4 photosynthetic metabolism

The goal of suppressing photorespiration in crops to maximize assimilation and yield is stimulating considerable interest among researchers looking to bioengineer carbon-concentrating mechanisms into C₃ plants. However, detailed quantification of the biochemical activities in the bundle sheath is lacking. This work presents a general stoichiometric model for C₃, C₂, C₂+C₄, and C₄ assimilation (SMA) in which energetics, metabolite traffic, and the different decarboxylating enzymes (NAD-dependent malic enzyme, NADP-dependent malic enzyme, or phosphoenolpyruvate carboxykinase) are explicitly included. The SMA can be used to refine experimental data analysis or formulate hypothetical scenarios, and is coded in a freely available Microsoft Excel workbook. The theoretical underpinnings and general model behaviour are analysed with a range of simulations, including (i) an analysis of C₃, C₂, C₂+C₄, and C₄ in operational conditions; (ii) manipulating photorespiration in a C₃ plant; (iii) progressively upregulating a C₂ shuttle in C₃ photosynthesis; (iv) progressively upregulating a C₄ cycle in C₂ photosynthesis; and (v) manipulating processes that are hypothesized to respond to transient environmental inputs. Results quantify the functional trade-offs, such as the electron transport needed to meet ATP/NADPH demand, as well as metabolite traffic, inherent to different subtypes. The SMA refines our understanding of the stoichiometry of photosynthesis, which is of paramount importance for basic and applied research.

Impact of anatomical traits of maize (Zea mays L.) leaf as affected by nitrogen supply and leaf age on bundle sheath conductance

The mechanism of photosynthesis in C₄ crops depends on the archetypal Kranz-anatomy. To examine how the leaf anatomy, as altered by nitrogen supply and leaf age, affects the bundle sheath conductance (g_bs), maize (Zea mays L.) plants were grown under three contrasting nitrogen levels. Combined gas exchange and chlorophyll fluorescence measurements were done on fully grown leaves at two leaf ages. The measured data were analysed using a biochemical model of C₄ photosynthesis to estimate g_bs. The leaf microstructure and ultrastructure were quantified using images obtained from micro-computed tomography and microscopy. There was a strong positive correlation between g_bs and leaf nitrogen content (LNC) while old leaves had lower g_bs than young leaves. Leaf thickness, bundle sheath cell wall thickness and surface area of bundle sheath cells per unit leaf area (S_b) correlated well with g_bs although they were not significantly affected by LNC. As a result, the increase of g_bs with LNC was little explained by the alteration of leaf anatomy. In contrast, the combined effect of LNC and leaf age on S_b was responsible for differences in g_bs between young leaves and old leaves. Future investigations should consider changes at the level of plasmodesmata and membranes along the CO₂ leakage pathway to unravel LNC and age effects further.

The Metabolite Pathway between Bundle Sheath and Mesophyll: Quantification of Plasmodesmata in Leaves of C3 and C4 Monocots

C4 photosynthesis is characterized by a CO2-concentrating mechanism between mesophyll (M) and bundle sheath (BS) cells of leaves. This generates high metabolic fluxes between these cells, through interconnecting plasmodesmata (PD). Quantification of these symplastic fluxes for modeling studies requires accurate quantification of PD, which has proven difficult using transmission electron microscopy. Our new quantitative technique combines scanning electron microscopy and 3D immunolocalization in intact leaf tissues to compare PD density on cell interfaces in leaves of C3 (rice [Oryza sativa] and wheat [Triticum aestivum]) and C4 (maize [Zea mays] and Setaria viridis) monocot species. Scanning electron microscopy quantification of PD density revealed that C4 species had approximately twice the number of PD per pitfield area compared with their C3 counterparts. 3D immunolocalization of callose at pitfields using confocal microscopy showed that pitfield area per M-BS interface area was 5 times greater in C4 species. Thus, the two C4 species had up to nine times more PD per M-BS interface area (S. viridis, 9.3 PD µm(-2); maize, 7.5 PD µm(-2); rice 1.0 PD µm(-2); wheat, 2.6 PD µm(-2)). Using these anatomical data and measured photosynthetic rates in these C4 species, we have now calculated symplastic C4 acid flux per PD across the M-BS interface. These quantitative data are essential for modeling studies and gene discovery strategies needed to introduce aspects of C4 photosynthesis to C3 crops.

Strategies for improving C4 photosynthesis

Recent activities to improve photosynthetic performance in crop plants has focused mainly on C3 photosynthesis where there are clear identified targets such as improving Rubisco kinetics, installation of a CO2 concentrating mechanism and alleviating limitations in chloroplast electron transport. Here we address strategies to improve photosynthetic performance in C4 plants, which utilize a CO2 concentrating mechanism, having evolved a complex blend of anatomy and biochemistry to achieve this. While the limitations to photosynthetic flux are not as well studied in C4 plants, work in transgenic Flaveria bidentis, a transformable model C4 dicot, and recent transcriptional analysis of leaves from diverse C4 plants, provides several gene candidates for improvement of carbon metabolism (such as pyruvate orthophosphate dikinase, phosphoenolpyruvate carboxylase and Rubisco) and for access of CO2 to phosphoenolpyruvate carboxylase in the mesophyll cells (such as carbonic anhydrase and CO2 porins). Chloroplast electron transport in C4 plants is shared between the two cell types, providing opportunities not only to alleviate limitations to flux through intersystem electron transport by targeting nuclear encoded proteins in the cytochrome (Cyt) b6/f complex, but in better sharing the harvesting of light energy between mesophyll and bundle sheath chloroplasts. Gene candidates for improvement of C4 photosynthesis could be utilized either through transgenic approaches or via mining natural allelic variation in sequenced populations of crop species.

Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice

The higher photosynthetic potential of C4 plants has led to extensive research over the past 50 years, including C4 -dominated natural biomes, crops such as maize, or for evaluating the transfer of C4 traits into C3 lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non-specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C4 photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C4 data analysis accessible to a broader audience. Outputs include those defining C4 photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO2 diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C4 organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd.

Plants in silico: why, why now and what?--an integrative platform for plant systems biology research

A paradigm shift is needed and timely in moving plant modelling from largely isolated efforts to a connected community endeavour that can take full advantage of advances in computer science and in mechanistic understanding of plant processes. Plants in silico (Psi) envisions a digital representation of layered dynamic modules, linking from gene networks and metabolic pathways through to cellular organization, tissue, organ and whole plant development, together with resource capture and use efficiency in dynamic competitive environments, ultimately allowing a mechanistically rich simulation of the plant or of a community of plants in silico. The concept is to integrate models or modules from different layers of organization spanning from genome to phenome to ecosystem in a modular framework allowing the use of modules of varying mechanistic detail representing the same biological process. Developments in high-performance computing, functional knowledge of plants, the internet and open-source version controlled software make achieving the concept realistic. Open source will enhance collaboration and move towards testing and consensus on quantitative theoretical frameworks. Importantly, Psi provides a quantitative knowledge framework where the implications of a discovery at one level, for example, single gene function or developmental response, can be examined at the whole plant or even crop and natural ecosystem levels.

A two-dimensional microscale model of gas exchange during photosynthesis in maize (Zea mays L.) leaves

CO2 exchange in leaves of maize (Zea mays L.) was examined using a microscale model of combined gas diffusion and C4 photosynthesis kinetics at the leaf tissue level. Based on a generalized scheme of photosynthesis in NADP-malic enzyme type C4 plants, the model accounted for CO2 diffusion in a leaf tissue, CO2 hydration and assimilation in mesophyll cells, CO2 release from decarboxylation of C4 acids, CO2 fixation in bundle sheath cells and CO2 retro-diffusion from bundle sheath cells. The transport equations were solved over a realistic 2-D geometry of the Kranz anatomy obtained from light microscopy images. The predicted responses of photosynthesis rate to changes in ambient CO2 and irradiance compared well with those obtained from gas exchange measurements. A sensitivity analysis showed that the CO2 permeability of the mesophyll-bundle sheath and airspace-mesophyll interfaces strongly affected the rate of photosynthesis and bundle sheath conductance. Carbonic anhydrase influenced the rate of photosynthesis, especially at low intercellular CO2 levels. In addition, the suberin layer at the exposed surface of the bundle sheath cells was found beneficial in reducing the retro-diffusion. The model may serve as a tool to investigate CO2 diffusion further in relation to the Kranz anatomy in C4 plants.

Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, we suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data, and we demonstrate that our method predicts fluxes that achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems.

The Coordination of Gene Expression within Photosynthesis Pathway for Acclimation of C4 Energy Crop Miscanthus lutarioriparius

As a promising candidate for the second-generation C4 energy crop, Miscanthus lutarioriparius has well acclimated to the water-limited and high-light Loess Plateau in China by improving photosynthesis rate and water use efficiency (WUE) compared to its native habitat along Yangtze River. Photosynthetic genes were demonstrated as one major category of the candidate genes underlying the physiological superiority. To further study how photosynthetic genes interact to improve the acclimation potential of M. lutarioriparius, population expression patterns within photosynthesis pathway were explored between one mild environment and one harsh environment. We found that 108 transcripts in assembled transcriptome of M. lutarioriparius were highly similar to genes in three Kyoto Encyclopedia of Genes and Genomes (KEGG) photosynthesis pathways of sorghum and maize. Phylogenetic analyses using sorghum, maize, rice, and Arabidopsis genes of dark reaction identified 23 orthologs and 30 paralogs of M. lutarioriparius photosynthetic genes. These genes were also clustered into two kinds of expression pattern. 87% of transcripts in dark reaction were up-regulated and all 14 chloroplast-encoded transcripts in light reaction increased degradation in the harsh environment compared to the mild environment. Moreover, 80.8% of photosynthetic transcripts were coordinated at transcription level under the two environments. Interestingly, LHCI and PSI were significantly correlated with F-ATPase and C4 cycle. Overall, this study indicates the coordinated expression between cyclic electron transport (consisting of LHCI, PSI, and ATPase) and CO2-concentrating mechanism (C4 cycle) could account for photosynthesis plasticity on M. lutarioriparius acclimation potential.

Meeting the global food demand of the future by engineering crop photosynthesis and yield potential

Increase in demand for our primary foodstuffs is outstripping increase in yields, an expanding gap that indicates large potential food shortages by mid-century. This comes at a time when yield improvements are slowing or stagnating as the approaches of the Green Revolution reach their biological limits. Photosynthesis, which has been improved little in crops and falls far short of its biological limit, emerges as the key remaining route to increase the genetic yield potential of our major crops. Thus, there is a timely need to accelerate our understanding of the photosynthetic process in crops to allow informed and guided improvements via in-silico-assisted genetic engineering. Potential and emerging approaches to improving crop photosynthetic efficiency are discussed, and the new tools needed to realize these changes are presented.

Fluxes through plant metabolic networks: measurements, predictions, insights and challenges

Although the flows of material through metabolic networks are central to cell function, they are not easy to measure other than at the level of inputs and outputs. This is particularly true in plant cells, where the network spans multiple subcellular compartments and where the network may function either heterotrophically or photoautotrophically. For many years, kinetic modelling of pathways provided the only method for describing the operation of fragments of the network. However, more recently, it has become possible to map the fluxes in central carbon metabolism using the stable isotope labelling techniques of metabolic flux analysis (MFA), and to predict intracellular fluxes using constraints-based modelling procedures such as flux balance analysis (FBA). These approaches were originally developed for the analysis of microbial metabolism, but over the last decade, they have been adapted for the more demanding analysis of plant metabolic networks. Here, the principal features of MFA and FBA as applied to plants are outlined, followed by a discussion of the insights that have been gained into plant metabolic networks through the application of these time-consuming and non-trivial methods. The discussion focuses on how a system-wide view of plant metabolism has increased our understanding of network structure, metabolic perturbations and the provision of reducing power and energy for cell function. Current methodological challenges that limit the scope of plant MFA are discussed and particular emphasis is placed on the importance of developing methods for cell-specific MFA.

The benefits of photorespiratory bypasses: how can they work?

Bypassing the photorespiratory pathway is regarded as a way to increase carbon assimilation and, correspondingly, biomass production in C3 crops. Here, the benefits of three published photorespiratory bypass strategies are systemically explored using a systems-modeling approach. Our analysis shows that full decarboxylation of glycolate during photorespiration would decrease photosynthesis, because a large amount of the released CO2 escapes back to the atmosphere. Furthermore, we show that photosynthesis can be enhanced by lowering the energy demands of photorespiration and by relocating photorespiratory CO2 release into the chloroplasts. The conductance of the chloroplast membranes to CO2 is a key feature determining the benefit of the relocation of photorespiratory CO2 release. Although our results indicate that the benefit of photorespiratory bypasses can be improved by increasing sedoheptulose bisphosphatase activity and/or increasing the flux through the bypass, the effectiveness of such approaches depends on the complex regulation between photorespiration and other metabolic pathways.